Check out Al Kavadlo's site for how to increase intensity with bodyweight exercises - the PBF ebook also mentions this. For example, instead of normal push-ups you can do plyometric push-ups, one arm push-ups and so forth. For the ultimate bodyweight strength you can look at advanced gymnastics with rings.
As far as Body by Science is concerned: I used to be a fan, then lost "faith" in it because I read a lot of critical opinions about it. Today I'm sure that the underlying principle is true:
You need to do infrequent, brief, intense workouts.
Having said that: I'd advise against P90X and CrossFit if your goal is to efficiently gain or maintain strength. Functional fitness is still a goal that many want to incorporate, but IMO you can best reach it by seeing it as "play" rather than "LHT". Do your infrequent HIT workouts, and in between do some infrequent bodyweight stuff, trying pull-ups, muscle-ups and the other stuff that requires strength and body control. You can go all out in the HIT workouts in a safe manner without the risk of injury, and in turn you can do bodyweight exercises on a level that you regard as "play", also keeping the risk of injury low. If you do CrossFit and constantly perform exercises in an all-out fashion that require excellent form and coordination in order not to injure yourself - you *will* at some point end up injuring yourself. Check out the CrossFit forum with its own section on injuries ...
BTW: HIT doesn't necessarily imply "superslow". Check out Drew Baye's excellent talk:
YouTube - Drew Baye T21C 2009 [Full] -- High Intensity Training Explained